From 0c3291937cdc896346bf703312d858b90db05a57 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:07:52 -0400 Subject: [PATCH 01/11] bump x.y.z version to even y prior to creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 554b667..a046c64 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.21.1 +Version: 1.22.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From 53bf075e1bb60ffaf4d359446972ee7bb3a464f1 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 30 Apr 2024 11:07:52 -0400 Subject: [PATCH 02/11] bump x.y.z version to odd y following creation of RELEASE_3_19 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index a046c64..8cdce10 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.22.0 +Version: 1.23.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From 5344b5ecbf43633686b5731da4940eac8d7d77e0 Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 29 Oct 2024 10:30:01 -0400 Subject: [PATCH 03/11] bump x.y.z version to even y prior to creation of RELEASE_3_20 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8cdce10..ad45066 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.23.0 +Version: 1.24.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From 21462a6cb4af1ac7556275e5c8077c130e98d16b Mon Sep 17 00:00:00 2001 From: J Wokaty Date: Tue, 29 Oct 2024 10:30:01 -0400 Subject: [PATCH 04/11] bump x.y.z version to odd y following creation of RELEASE_3_20 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index ad45066..76ad211 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.24.0 +Version: 1.25.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From 1eb7a0fceee40508a93f32e0ea03ec8fe302fbd9 Mon Sep 17 00:00:00 2001 From: A Wokaty Date: Tue, 15 Apr 2025 11:35:26 -0400 Subject: [PATCH 05/11] bump x.y.z version to even y prior to creation of RELEASE_3_21 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 76ad211..963eadb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.25.0 +Version: 1.26.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From f98263f9f25597aa4142448d827963f14fc7792b Mon Sep 17 00:00:00 2001 From: A Wokaty Date: Tue, 15 Apr 2025 11:35:26 -0400 Subject: [PATCH 06/11] bump x.y.z version to odd y following creation of RELEASE_3_21 branch --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 963eadb..fcf9469 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.26.0 +Version: 1.27.0 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From bdab7a5a0951945f205527058ecf3711ccafd56d Mon Sep 17 00:00:00 2001 From: zhewa Date: Fri, 26 Sep 2025 10:31:38 -0400 Subject: [PATCH 07/11] fix invalid class "GGbio" object: invalid object for slot "ggplot" --- DESCRIPTION | 2 +- R/rview.R | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 963eadb..0c44fdc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -20,7 +20,7 @@ Depends: R (>= 4.0) License: MIT + file LICENSE Encoding: UTF-8 LazyData: TRUE -RoxygenNote: 7.3.1 +RoxygenNote: 7.3.3 VignetteBuilder: knitr Imports: data.table, GenomicAlignments, diff --git a/R/rview.R b/R/rview.R index 9f00079..b30aea0 100644 --- a/R/rview.R +++ b/R/rview.R @@ -33,8 +33,8 @@ rview <- function(bamGA, S4Vectors::mcols(readsGr)$umi <- data.table::last( data.table::tstrsplit(names(readsGr), ":")) - g <- ggplot2::ggplot(readsGr) + - ggbio::geom_arrow(ggplot2::aes(color = umi)) + + g <- ggplot2::ggplot() + + ggbio::geom_arrow(data = readsGr, ggplot2::aes(color = umi)) + .themePublication() + ggplot2::theme(axis.title.y = ggplot2::element_blank()) From 3bdf082f5025e8101ac43118ed6e45d26d895f59 Mon Sep 17 00:00:00 2001 From: zhewa Date: Fri, 26 Sep 2025 11:18:50 -0400 Subject: [PATCH 08/11] use patchwork to combine plots in vignette --- DESCRIPTION | 3 ++- R/scruffFunctions.R | 8 +++++--- vignettes/scruff.Rmd | 14 +++++++++++--- 3 files changed, 18 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0c44fdc..99b3c8d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -47,7 +47,8 @@ Imports: data.table, SingleCellExperiment, SummarizedExperiment, Rsubread, - parallelly + parallelly, + patchwork Suggests: BiocStyle, knitr, diff --git a/R/scruffFunctions.R b/R/scruffFunctions.R index d149d22..5f4f0aa 100644 --- a/R/scruffFunctions.R +++ b/R/scruffFunctions.R @@ -386,9 +386,11 @@ size = ggplot2::rel(1), hjust = 0.5), text = ggplot2::element_text(), - panel.background = ggplot2::element_rect(color = NA), - plot.background = ggplot2::element_rect(color = NA), - panel.border = ggplot2::element_rect(color = NA), + panel.background = ggplot2::element_rect(fill = NA, + color = NA), + plot.background = ggplot2::element_rect(fill = NA, + color = NA), + panel.border = ggplot2::element_blank(), axis.title = ggplot2::element_text( face = "bold", size = ggplot2::rel(1)), diff --git a/vignettes/scruff.Rmd b/vignettes/scruff.Rmd index b0254de..3d063bc 100644 --- a/vignettes/scruff.Rmd +++ b/vignettes/scruff.Rmd @@ -26,6 +26,7 @@ suppressPackageStartupMessages(library(BiocStyle)) # For generation of these files, please refer to the Stepwise Tutorial. library(scruff) +library(patchwork) # Get the paths to example FASTQ, FASTA, and GTF files. # Please note that because the following files are included in @@ -220,9 +221,16 @@ data(bamExample, package = "scruff") start <- 1094 end <- 2675 -g1 <- rview(bamExample, chr = "MT", start = start, end = end) -g2 <- gview(gtf, chr = "MT", start = start, end = end) -g <- ggbio::tracks(g1, g2, heights = c(4, 1), xlab = "chr MT") +g1 <- rview(bamExample, chr = "MT", start = start, end = end) + + ggplot2::scale_x_continuous(limits = c(start, end)) +g2 <- gview(gtf, chr = "MT", start = start, end = end) + + ggplot2::scale_x_continuous(limits = c(start, end)) +g <- (g1 + ggplot2::theme(axis.title.x = ggplot2::element_blank(), + axis.text.x = ggplot2::element_blank(), + plot.margin = ggplot2::margin(t = 0, b = 0))) / + (g2 + ggplot2::theme(plot.margin = ggplot2::margin(t = 0, b = 0))) / + patchwork::plot_layout(ncol = 1, + heights = c(4, 1)) g ``` From 148d3a315f78ffba136b57f76125520c44d05807 Mon Sep 17 00:00:00 2001 From: zhewa Date: Fri, 26 Sep 2025 11:24:26 -0400 Subject: [PATCH 09/11] version bump --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index fcf9469..0aa2471 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scruff Title: Single Cell RNA-Seq UMI Filtering Facilitator (scruff) -Version: 1.27.0 +Version: 1.27.1 Date: 2024-03-27 Authors@R: c(person("Zhe", "Wang", email = "zhe@bu.edu", From 7c124a29315013e182170b3b9df95cd54da3c47b Mon Sep 17 00:00:00 2001 From: Zhe Wang Date: Mon, 29 Sep 2025 17:04:00 -0400 Subject: [PATCH 10/11] update github actions --- .github/workflows/R-CMD-check.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a1fef09..9cc0edc 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -27,11 +27,11 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} @@ -44,7 +44,7 @@ jobs: sudo apt-get install --yes libcurl4-openssl-dev Rscript -e "install.packages('curl', repos='https://cloud.r-project.org')" - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: rcmdcheck From 9486e9f9e77cd62389f4f18c14da711495929cc0 Mon Sep 17 00:00:00 2001 From: Zhe Wang Date: Mon, 29 Sep 2025 17:15:59 -0400 Subject: [PATCH 11/11] update check-r-package@v2 --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9cc0edc..071de2f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -48,7 +48,7 @@ jobs: with: extra-packages: rcmdcheck - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 - name: Show testthat output if: always()